Variant report

Variant	rs11564297
Chromosome Location	chr18:25643698-25643699
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10502507	0.83[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1078501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10853680	0.80[EUR][1000 genomes]
rs10853681	0.83[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11083245	0.80[CEU][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11083246	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11083248	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1122356	0.94[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap]
rs1148376	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11564308	0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs11564316	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11564329	0.83[CEU][hapmap];0.82[CHB][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11564330	0.81[EUR][1000 genomes]
rs11564332	0.80[EUR][1000 genomes]
rs11564396	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11564397	1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11564400	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11564405	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11564409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11564412	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs11564413	0.80[EUR][1000 genomes]
rs11873053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1220015	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1220016	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1220019	0.90[ASN][1000 genomes]
rs1228419	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1234682	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12958882	0.80[EUR][1000 genomes]
rs1373136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1373138	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1443450	0.81[EUR][1000 genomes]
rs1443451	0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs1443453	0.80[TSI][hapmap]
rs17445875	0.80[EUR][1000 genomes]
rs17446001	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs17446316	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17463213	0.83[CEU][hapmap];0.82[CHB][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17463233	0.83[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17463295	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17468531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17468636	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1808940	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1816825	0.88[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1838161	0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs1867285	0.83[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1941180	0.81[EUR][1000 genomes]
rs1944292	0.83[CEU][hapmap];0.82[CHB][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1944294	0.82[CHB][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs1972934	1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2053599	0.83[CEU][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2156605	0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs2218361	0.82[EUR][1000 genomes]
rs2310784	0.80[EUR][1000 genomes]
rs2920447	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4144654	0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs4598992	0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs4800838	0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs4800839	0.80[EUR][1000 genomes]
rs4800840	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4800841	1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs490820	0.94[CHB][hapmap]
rs500643	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs533602	1.00[CHB][hapmap]
rs539075	1.00[CHB][hapmap]
rs565509	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs568575	1.00[CHB][hapmap]
rs576467	0.94[CHB][hapmap]
rs584936	0.94[CHB][hapmap]
rs587526	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs587613	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs597591	0.94[CHB][hapmap];0.88[CHD][hapmap]
rs602819	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs610906	0.96[ASN][1000 genomes]
rs614966	0.94[CHB][hapmap];0.88[CHD][hapmap]
rs623234	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs643555	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs647733	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs656642	0.94[CHB][hapmap]
rs665651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs665781	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs673008	0.94[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.82[TSI][hapmap]
rs683457	0.96[ASN][1000 genomes]
rs694943	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7230771	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7237382	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs72639459	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8087457	0.88[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap]
rs8087860	0.88[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8091314	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8091763	0.81[EUR][1000 genomes]
rs8092004	0.81[EUR][1000 genomes]
rs874314	0.80[EUR][1000 genomes]
rs894679	1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9635986	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9789154	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9789221	0.83[CEU][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761996	chr18:24866083-25818618	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11564297	RCAN3	trans	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:25625800-25650400	Weak transcription	Right Atrium	heart
2	chr18:25627600-25645600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr18:25641200-25645000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr18:25641400-25645000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr18:25641600-25644200	Weak transcription	Left Ventricle	heart
6	chr18:25642200-25643800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr18:25642400-25646800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr18:25642400-25646800	Enhancers	HSMM	muscle
9	chr18:25642600-25643800	Enhancers	H1 Cell Line	embryonic stem cell
10	chr18:25642600-25643800	Enhancers	Brain Anterior Caudate	brain
11	chr18:25642600-25644000	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr18:25642600-25644000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr18:25642600-25644000	Enhancers	Brain Substantia Nigra	brain
14	chr18:25642600-25644200	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr18:25642600-25645000	Enhancers	Ovary	ovary
16	chr18:25642600-25645000	Enhancers	Osteobl	bone
17	chr18:25642600-25646200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr18:25642600-25646800	Enhancers	Fetal Heart	heart
19	chr18:25642800-25643800	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr18:25642800-25643800	Enhancers	Brain Angular Gyrus	brain
21	chr18:25642800-25644000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr18:25642800-25644000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr18:25642800-25644000	Enhancers	NHLF	lung
24	chr18:25642800-25644800	Enhancers	HSMMtube	muscle
25	chr18:25642800-25646200	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr18:25642800-25647400	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr18:25643000-25643800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr18:25643000-25645000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr18:25643000-25655200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr18:25643200-25643800	Enhancers	H9 Cell Line	embryonic stem cell
31	chr18:25643200-25643800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr18:25643200-25643800	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr18:25643200-25643800	Enhancers	Brain Cingulate Gyrus	brain
34	chr18:25643200-25643800	Enhancers	Brain Germinal Matrix	brain
35	chr18:25643200-25643800	Enhancers	Placenta Amnion	Placenta Amnion
36	chr18:25643200-25644000	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr18:25643200-25644000	Enhancers	Fetal Kidney	kidney
38	chr18:25643200-25644200	Enhancers	HUVEC	blood vessel
39	chr18:25643200-25644800	Enhancers	A549	lung
40	chr18:25643200-25645800	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr18:25643200-25646000	Enhancers	Brain Hippocampus Middle	brain
42	chr18:25643200-25646600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr18:25643200-25646800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr18:25643200-25647400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr18:25643400-25643800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr18:25643400-25643800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr18:25643400-25644200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr18:25643400-25644200	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr18:25643400-25644200	Enhancers	Fetal Lung	lung
50	chr18:25643400-25644200	Enhancers	HepG2	liver

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